Looks like this was a bug that was introduced some time ago when we added our sort cache. PM reads the sub-seconds Exif tag which some manufactures include (e.g Nikon) but not all do. This is used for sorting by capture time in addition to the normal timestamp (which is only good to the second). If sorting by capture time and the second (or second+ss) match, then PM is supposed to fall back to filename. As you pointed out, sorting by filename won't work for multiple camera bodies. The bug was causing the ss part to always be 00 instead of 00..99.
Anyway, Kirk found the problem and we will update in the next build. In the meantime, you can try a custom sort by using "{date sort}{timesortlong}" instead. This might be just a little bit slower.
HTH,
--dennis